bloom-lims 2.0.0

Templated Abstract Polymorphic LIMS - A Laboratory Information Management System

Bloom

Bloom is the wet-lab and material-state authority in this workspace.

It owns the physical side of the beta LIMS flow:

• containers and placements
• specimens and derived materials
• extraction, QC, library-prep, pool, and run objects
• sequenced library assignments
• wet-lab queue membership and queue-transition state
• Bloom-side lineage linking to Atlas fulfillment context

It does not own:

• customer-portal data and tenant administration
• patient, clinician, shipment, TRF, or test truth
• artifact registry authority
• analysis execution or result-return workflows

Runtime Shape

Bloom is a FastAPI application with both API and server-rendered GUI surfaces.

Primary entrypoints:

• app entrypoint: main.py
• app factory: bloom_lims.app:create_app
• CLI entrypoint: bloom

Primary CLI groups:

• bloom server: start, stop, status, logs
• bloom db: TapDB lifecycle and Bloom template seeding
• bloom integrations atlas: show and validate Atlas integration config
• bloom test, bloom quality, bloom users, bloom config

API Surface

Canonical API router prefix: /api/v1

Core route groups mounted today:

• /api/v1/objects
• /api/v1/containers
• /api/v1/content
• /api/v1/equipment
• /api/v1/templates
• /api/v1/subjects
• /api/v1/lineages
• /api/v1/search
• /api/v1/search/v2
• /api/v1/object-creation
• /api/v1/tracking
• /api/v1/user-tokens
• /api/v1/admin/*
• /api/v1/external/specimens
• /api/v1/external/atlas
• /api/v1/external/atlas/beta

Server-rendered GUI routes remain active under the root app, including login, operational views, and graph screens.

Cross-Repo Boundaries

• Atlas sends accepted-material and status traffic into Bloom.
• Bloom links physical execution state back to Atlas TRF/test/fulfillment-item context.
• Bloom can register run artifacts in Dewey when Dewey integration is enabled.
• Ursa resolves sequencing context from Bloom using run and lane identifiers.

TapDB Mount

Bloom can mount the TapDB admin surface inside the same server process.

Mounted path defaults to /admin/tapdb.

Mounted-mode rules:

• Bloom session auth is the gate.
• access is admin-only
• unauthenticated browser requests redirect to /login
• mounted TapDB local login is disabled

Timezone Policy

• Bloom persists timestamps in UTC.
• display timezone is user-configurable via TapDB-backed system_user preferences
• canonical preference key: display_timezone

Local Development

Typical local flow:

source bloom_activate.sh
pip install -e .
bloom db build
bloom server start --foreground

Focused validation commands:

source bloom_activate.sh
pytest --no-cov tests/test_api_atlas_bridge.py tests/test_atlas_lookup_resilience.py tests/test_queue_flow.py tests/test_run_resolver.py tests/test_beta_cross_repo_smoke.py
ruff check bloom_lims tests

Current Docs

• Docs index
• Bloom beta API contracts
• Search V2
• Authentication

Historical execution plans remain in docs/, but they are reference material rather than the primary source of truth.